Amelioration of bacterial genomes: Rates of change and exchange
Amelioration of bacterial genomes: Rates of change and exchange
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DOI：
10.1007/pl00006158
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发表时间：
1997-04-01
影响因子：
3.9
通讯作者：
Ochman, H
中科院分区：
文献类型：
--
作者：
Lawrence, JG;Ochman, H
尽管细菌物种的总GC含量存在很大差异，但特定物种基因组内的基因在碱基组成上相对相似。因此，细菌基因组的新颖序列（即通过最近水平转移引入的 DNA）通常具有不寻常的序列特征，并且可以与祖先 DNA 区分开来。在基因渗入时，水平转移的基因反映了供体基因组的碱基组成；但是，随着时间的推移，这些序列将得到改善，以反映新基因组的 DNA 组成，因为渗入的基因会经历影响受体基因组中所有基因的相同突变过程。这种改善过程在涉及肠道细菌入侵宿主细胞的大量基因中很明显，并且可以建模来预测外源 DNA 转移后与天然 DNA 相似所需的时间。此外，改善模型可用于估计外源基因渗入染色体的时间。将这种方法应用于 1.43 兆碱基的连续序列，我们计算出整个大肠杆菌染色体包含超过 600 kb 的水平转移的蛋白质编码 DNA。对改良时间的估计表明，这种 DNA 以每百万年 31 kb 的速度积累，与点突变引入的变异 DNA 的数量级相当。这个速度预测，大肠杆菌和肠沙门氏菌谱系自分歧以来，各自获得和丢失了超过 3 兆碱基的新 DNA，
Although bacterial species display wide variation in their overall GC contents, the genes within a particular species' genome are relatively similar in base composition. As a result, sequences that are novel to a bacterial genome-i.e., DNA introduced through recent horizontal transfer-often bear unusual sequence characteristics and can be distinguished from ancestral DNA. At the time of introgression, horizontally transferred genes reflect the base composition of the donor genome; but, over time, these sequences will ameliorate to reflect the DNA composition of the new genome because the introgressed genes are subject to the same mutational processes affecting all genes in the recipient genome. This process of amelioration is evident in a large group of genes involved in host-cell invasion by enteric bacteria and can be modelled to predict the amount of time required after transfer for foreign DNA to resemble native DNA. Furthermore, models of amelioration can be used to estimate the time of introgression of foreign genes in a chromosome. Applying this approach to a 1.43-megabase continuous sequence, we have calculated that the entire Escherichia coli chromosome contains more than 600 kb of horizontally transferred, protein-coding DNA. Estimates of amelioration times indicate that this DNA has accumulated at a rate of 31 kb per million years, which is on the order of the amount of variant DNA introduced by point mutations, This rate predicts that the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases of novel DNA since their divergence,